I try not to advertise them, because I'm possessive of them, but zoorama in the Bronx is a great little LFS.

I get along really well with the people there. I give them a lot of my fish for store credit. They do have a pretty decent selection of plants, not as good as Pacific though. The prices are high, but not insanely so, and you can haggle a little. If the door is locked just go down the block to where they sell the big animals and someone will let you in.